Chemical Components in the PDB

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T5X : Summary

Code

T5X

One-letter code

X

Molecule name

2-C-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thia zol-3-ium-2-yl}-5-O-phosphono-D-xylitol

Synonyms

D-XYLULOSE-5-PHOSPHATE THIAMIN DIPHOSPHATE ADDUCT

Systematic names

ProgramVersionName
ACDLabs 10.04 2-C-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium-2-yl}-5-O-phosphono-D-xylitol
OpenEye OEToolkits 1.5.0 2-[3-[(4-amino-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2-[(2S,3S,4R)-1,2,3,4-tetrahydroxy-5-phosphonooxy-pentan-2-yl]-1,3-thiazol-3-ium-5-yl]ethyl phosphono hydrogen phosphate

Formula

C17 H30 N4 O15 P3 S

Formal charge

1

Molecular weight

655.424 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)OCC(O)C(O)C(O)(c1sc(c([n+]1Cc2cnc(nc2N)C)C)CCOP(=O)(O)OP(=O)(O)O)CO
SMILES CACTVS 3.341 Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C](O)(CO)[CH](O)[CH](O)CO[P](O)(O)=O)c(N)n1
SMILES OpenEye OEToolkits 1.5.0 Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(CO)(C(C(COP(=O)(O)O)O)O)O)CCOP(=O)(O)OP(=O)(O)O
Canonical SMILES CACTVS 3.341 Cc1ncc(C[n+]2c(C)c(CCO[P@](O)(=O)O[P](O)(O)=O)sc2[C@](O)(CO)[C@@H](O)[C@H](O)CO[P](O)(O)=O)c(N)n1
Canonical SMILES OpenEye OEToolkits 1.5.0 Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@](CO)([C@H]([C@@H](COP(=O)(O)O)O)O)O)CCO[P@@](=O)(O)OP(=O)(O)O

IUPAC InChI

InChI=1S/C17H29N4O15P3S/c1-9-13(3-4-34-39(32,33)36-38(29,30)31)40-16(21(9)6-11-5-19-10(2)20-15(11)18)17(25,8-22)14(24)12(23)7-35-37(26,27)28/h5,12,14,22-25H,3-4,6-8H2,1-2H3,(H6-,18,19,20,26,27,28,29,30,31,32,33)/p+1/t12-,14+,17+/m1/s1

IUPAC InChI key

CRLXIEJPMQNLRP-IFIJOSMWSA-O
T5X

wwPDB Information

Atom count

70 (40 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2007-10-25

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



T5X : Atoms of Molecule

Total Number of Atoms: 70
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O2A O O2A N N N 0 -4.744 -2.721 -1.455
2 PA P PA R N N 0 -5.304 -1.671 -0.37
3 O1A O O1A N N N 0 -5.644 -0.399 -1.044
4 O3A O O3A N N N 0 -6.622 -2.276 0.331
5 PB P PB N N N 0 -8.15 -2.468 -0.138
6 O3B O O3B N N N 0 -8.901 -1.045 -0.116
7 O2B O O2B N N N 0 -8.179 -3.02 -1.511
8 O1B O O1B N N N 0 -8.895 -3.484 0.864
9 O7 O O7 N N N 0 -4.177 -1.402 0.748
10 C7 C C7 N N N 0 -2.929 -0.77 0.458
11 C6 C C6 N N N 0 -2.098 -0.671 1.739
12 C5 C C5 N Y N 0 -0.781 -0.005 1.433
13 S1 S S1 N Y N 0 0.702 -0.818 0.938
14 C2 C C2 N Y N 0 1.509 0.687 0.856
15 CX2 C CX2 S N N 0 2.954 0.87 0.467
16 CX3 C CX3 S N N 0 3.618 -0.499 0.312
17 CX4 C CX4 R N N 0 5.113 -0.313 0.045
18 CX5 C CX5 N N N 0 5.8 -1.68 0.021
19 OX5 O OX5 N N N 0 7.212 -1.501 -0.113
20 PX P PX N N N 0 8.25 -2.73 -0.173
21 OX7 O OX7 N N N 0 8.064 -3.591 1.016
22 OX6 O OX6 N N N 0 7.985 -3.592 -1.507
23 OX8 O OX8 N N N 0 9.756 -2.16 -0.192
24 OX4 O OX4 N N N 0 5.295 0.334 -1.216
25 OX3 O OX3 N N N 0 3.022 -1.197 -0.783
26 CX1 C CX1 N N N 0 3.032 1.628 -0.859
27 OX1 O OX1 N N N 0 2.308 0.912 -1.861
28 OX2 O OX2 N N N 0 3.629 1.615 1.482
29 N3 N N3 N Y N 1 0.703 1.642 1.175
30 C4 C C4 N Y N 0 -0.534 1.307 1.484
31 CM4 C CM4 N N N 0 -1.581 2.32 1.867
32 C7, C C7, N N N 0 1.142 3.04 1.187
33 C5, C C5, N Y N 0 0.298 3.839 0.227
34 C4, C C4, N Y N 0 -0.632 4.769 0.695
35 N4, N N4, N N N 0 -0.798 4.976 2.055
36 N3, N N3, N Y N 0 -1.356 5.455 -0.185
37 C2, C C2, N Y N 0 -1.201 5.261 -1.479
38 CM2 C CM2 N N N 0 -2.04 6.057 -2.445
39 N1, N N1, N Y N 0 -0.331 4.391 -1.952
40 C6, C C6, N Y N 0 0.43 3.674 -1.138
41 HO2A H HO2A N N N 0 -4.501 -3.579 -1.082
42 HO3B H HO3B N N N 0 -8.921 -0.624 0.754
43 HO1B H HO1B N N N 0 -9.822 -3.647 0.641
44 H71 H 1H7 N N N 0 -2.387 -1.359 -0.282
45 H72 H 2H7 N N N 0 -3.111 0.23 0.064
46 H61 H 1H6 N N N 0 -2.64 -0.082 2.479
47 H62 H 2H6 N N N 0 -1.916 -1.671 2.133
48 HX3 H HX3 N N N 0 3.481 -1.075 1.227
49 HX4 H HX4 N N N 0 5.55 0.299 0.834
50 HX51 H 1HX5 N N N 0 5.588 -2.21 0.949
51 HX52 H 2HX5 N N N 0 5.427 -2.26 -0.823
52 HOX6 H HOX6 N N N 0 8.089 -3.09 -2.326
53 HOX8 H HOX8 N N N 0 10.436 -2.847 -0.228
54 HOX4 H HOX4 N N N 0 4.93 -0.156 -1.966
55 HOX3 H HOX3 N N N 0 3.22 -0.813 -1.648
56 HX11 H 1HX1 N N N 0 2.598 2.621 -0.737
57 HX12 H 2HX1 N N N 0 4.075 1.723 -1.163
58 HOX1 H HOX1 N N N 0 2.315 1.335 -2.73
59 HOX2 H HOX2 N N N 0 3.619 1.193 2.352
60 HM41 H 1HM4 N N N 0 -1.464 2.584 2.918
61 HM42 H 2HM4 N N N 0 -1.464 3.214 1.254
62 HM43 H 3HM4 N N N 0 -2.572 1.896 1.707
63 H7,1 H 1H7, N N N 0 1.032 3.447 2.192
64 H7,2 H 2H7, N N N 0 2.187 3.095 0.884
65 H4,1 H 1H4, N N N 0 -0.175 4.581 2.685
66 H4,2 H 2H4, N N N 0 -1.536 5.515 2.377
67 HM21 H 1HM2 N N N 0 -1.522 6.981 -2.701
68 HM22 H 2HM2 N N N 0 -2.207 5.472 -3.349
69 HM23 H 3HM2 N N N 0 -2.999 6.294 -1.983
70 H6, H H6, N N N 0 1.14 2.964 -1.537



T5X : Chemical Bonds

Total Number of Bonds: 71
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O1A PA O P doub 1.48 N N
2 O2B PB O P doub 1.48 N N
3 PA O7 P O sing 1.61 N N
4 PA O2A P O sing 1.61 N N
5 PA O3A P O sing 1.61 N N
6 O7 C7 O C sing 1.43 N N
7 PB O1B P O sing 1.61 N N
8 PB O3A P O sing 1.61 N N
9 PB O3B P O sing 1.61 N N
10 C7 C6 C C sing 1.53 N N
11 C6 C5 C C sing 1.51 N N
12 CM4 C4 C C sing 1.51 N N
13 C5 C4 C C doub 1.34 N Y
14 C5 S1 C S sing 1.76 N Y
15 C4 N3 C N sing 1.32 N Y
16 N1, C6, N C doub 1.33 N Y
17 N1, C2, N C sing 1.32 N Y
18 C6, C5, C C sing 1.38 N Y
19 S1 C2 S C sing 1.71 N Y
20 N3 C7, N C sing 1.47 N N
21 N3 C2 N C doub 1.29 N Y
22 CM2 C2, C C sing 1.51 N N
23 C2, N3, C N doub 1.32 N Y
24 C5, C7, C C sing 1.51 N N
25 C5, C4, C C doub 1.4 N Y
26 C2 CX2 C C sing 1.51 N N
27 N3, C4, N C sing 1.33 N Y
28 C4, N4, C N sing 1.39 N N
29 OX3 CX3 O C sing 1.43 N N
30 CX3 CX2 C C sing 1.53 N N
31 CX3 CX4 C C sing 1.53 N N
32 CX2 CX1 C C sing 1.53 N N
33 CX2 OX2 C O sing 1.43 N N
34 CX1 OX1 C O sing 1.43 N N
35 CX5 CX4 C C sing 1.53 N N
36 CX5 OX5 C O sing 1.43 N N
37 OX7 PX O P doub 1.48 N N
38 CX4 OX4 C O sing 1.43 N N
39 OX5 PX O P sing 1.61 N N
40 PX OX8 P O sing 1.61 N N
41 PX OX6 P O sing 1.61 N N
42 O2A HO2A O H sing 0.97 N N
43 O3B HO3B O H sing 0.97 N N
44 O1B HO1B O H sing 0.97 N N
45 C7 H71 C H sing 1.09 N N
46 C7 H72 C H sing 1.09 N N
47 C6 H61 C H sing 1.09 N N
48 C6 H62 C H sing 1.09 N N
49 CX3 HX3 C H sing 1.09 N N
50 CX4 HX4 C H sing 1.09 N N
51 CX5 HX51 C H sing 1.09 N N
52 CX5 HX52 C H sing 1.09 N N
53 OX6 HOX6 O H sing 0.97 N N
54 OX8 HOX8 O H sing 0.97 N N
55 OX4 HOX4 O H sing 0.97 N N
56 OX3 HOX3 O H sing 0.97 N N
57 CX1 HX11 C H sing 1.09 N N
58 CX1 HX12 C H sing 1.09 N N
59 OX1 HOX1 O H sing 0.97 N N
60 OX2 HOX2 O H sing 0.97 N N
61 CM4 HM41 C H sing 1.09 N N
62 CM4 HM42 C H sing 1.09 N N
63 CM4 HM43 C H sing 1.09 N N
64 C7, H7,1 C H sing 1.09 N N
65 C7, H7,2 C H sing 1.09 N N
66 N4, H4,1 N H sing 0.97 N N
67 N4, H4,2 N H sing 0.97 N N
68 CM2 HM21 C H sing 1.09 N N
69 CM2 HM22 C H sing 1.09 N N
70 CM2 HM23 C H sing 1.09 N N
71 C6, H6, C H sing 1.08 N N



T5X : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
T5X 2r8o Open in New Window Bound ligand 2 1
T5X 5xqk Open in New Window Bound ligand 1 1